Background: Health economic assessments are used to determine whether the resources needed to generate net benefit from a screening programme, driven by multiple complex benefits and harms, are justifiable. We sys-tematically identified the benefits and harms incorporated within economic assessments evaluating antenatal and newborn screening programmes. Methods: For this systematic review and thematic analysis, we searched the published and grey literature from January 2000 to January 2021. Studies that included an economic evaluation of an antenatal or newborn screening programme in an OECD country were eligible. We identified benefits and harms using an integrative descriptive analysis, and illustrated a thematic framework. (Systematic review registration PROSPERO, CRD42020165236). Findings: The searches identified 52,244 articles and reports and 336 (242 antenatal and 95 newborn) were included. Eighty-six subthemes grouped into seven themes were identified: 1) diagnosis of screened for condi-tion, 2) life years and health status adjustments, 3) treatment, 4) long-term costs, 5) overdiagnosis, 6) pregnancy loss, and 7) spillover effects on family members. Diagnosis of screened for condition (115 studies, 47.5%), life -years and health status adjustments (90 studies, 37.2%) and treatment (88 studies, 36.4%) accounted for most of the benefits and harms evaluating antenatal screening. The same themes accounted for most of the benefits and harms included in studies assessing newborn screening. Overdiagnosis and spillover effects tended to be ignored. Interpretation: Our proposed framework can be used to guide the development of future health economic as-sessments evaluating antenatal and newborn screening programmes, to prevent exclusion of important potential benefits and harms.